Analysis of Transposable elements


14th-18th June 2021

Due to the COVID-19 outbreak, this course will be held online


General Topic: Evolution of transposable elements and their de-novo annotation in non-model genomes


Transposable elements (TEs) are selfish genetic elements which exist in virtually all eukaryotic genomes. Because TEs contain regulatory or coding sequence for their own ‘survival’ and often occur in large numbers within a genome, they can have strong effects on the transcription or methylation of nearby genes and significantly promote structural variation or genome size expansion. Accurate annotation of TEs is thus important for many studies in genomics and evolutionary biology. However, TEs are rapidly evolving due to arms races with their host genomes and thus often remain undetected in newly sequenced genomes. One may argue that in-depth annotation of TEs is currently one of the biggest bottlenecks in genomics research of non-model organisms. This is because computational TE analyses require knowledge of TE biology as well as some degree of manual curation to overcome incomplete or erroneous annotations. The present course aims to adress this bottleneck by teaching TE biology, computational analyses of TEs in genome assemblies (RepeatModeler, RepeatMasker) and raw read data (dnaPipeTE), and manual analyses of TEs (consensus curation, classification).



At the end of this course, attendants should be able to conduct computational analyses of TEs, interpret the results in the light of TE biology, and improve TE annotations through manual curation. To achieve this, the first three days of the course will provide lectures and practicals on all these topics. The last two days of the course consist entirely of supervised individual practicals to further refine the attendants’ skills in computational and manual analyses of TEs, either in their own data or in a course-specific collaborative project. Participation in the collaborative project will be acknowledged through co-authorship on a planned TE manuscript.



The course is aimed at biologists on the PhD student and postdoc level who are new to TE analyses and/or de-novo annotation of the repetitive fraction of non-model genomes.



Attendants will need to use the command line and a sequence alignment program (e.g., BioEdit) on their laptops. Basic knowledge of these will be helpful but is not required. Attendants are encouraged to bring their own genome assembly and/or raw read data but are welcome to join the collaborative project.





Monday 14th CET – Day 1:


14:00 - 14:45 Lecture on TE diversity

14:45 - 15:30 Lecture on TE mechanisms

15:30 - 16:00 Break

16:00 - 18:00 Practical on repeat prediction (esp. RepeatModeler/RepeatMasker) (I)

18:00 - 18:30 Break

18:30 - 20:00 Practical on repeat prediction (esp. RepeatModeler/RepeatMasker) (II)




Dr. Alexander Suh




Teaching Assistant


Valentina Peona




Cost overview

Cancellation Policy:


> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.


Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.